Stargate Atlantis: Journeys for Pegasus
by Obrusnine
Summary: Atlantis's business in the Pegasus galaxy is not yet finished. The team will need to battle against conflict on all sides in order to finally defeat the Wraith and bring peace to the Pegasus galaxy. This story is an ongoing episodic series of twenty episodes. It will be part of a group of four stories meant to finally give Stargate the ending it deserves. New scene every Friday!
1. S06E01: Chronicles - Part I

**_This story is based on my want as a Stargate fan for a legitimate conclusion to the Stargate franchise that I can be wholly satisfied with. There will be Twenty Episodes to total around a Season for each of the four stories that will contribute, one based on each of the Stargate television shows. Each Episode will be between 5 and 7 thousand words long and will be mostly focused on dialogue to drive the story forward, much like a script, but not completely. Each of these stories takes place in a shared universe, just like the television shows._**

 ** _All books and comics related to the television shows are things I do not consider canon for the sake of this story. As such, this story will be assembled from wholly original ideas (and of course ideas for future seasons pulled from Joseph Mallozzi's blogs that I have iterated on)._**

* * *

 ** _STARGATE ATLANTIS: JOURNEYS FOR PEGASUS_**

 _Summary: Atlantis's business in the Pegasus galaxy is not yet finished. The Atlantis team will need to battle against conflict on all sides in order to finally defeat the Wraith and bring peace to the Pegasus galaxy._

 ** _New Episodes every Friday evening at 8PM EST_**

* * *

 ** _STARGATE SG-1: UPRISING_**

 _Summary: A young hacker exposes the Stargate program to the general public, throwing Earth into chaos. The flagship team of Stargate command must work together with him to bring peace back to the planet and finally make the Tau'ri into the Fifth Race that the Asgard envisioned._

 ** _Will premier Monday, September 12th_**

 ** _New Episodes every Tuesday evening at 8PM EST_**

* * *

 ** _STARGATE UNIVERSE: THE LEGACY COMMAND_**

 _Summary: After finally reaching a new galaxy, the team aboard the Destiny must work together to not only solve the mystery behind the CMBR, but contend with a new advanced alien enemy by finally bringing the Destiny to its full potential._

 ** _Will premier Monday, January 30th, 2017_**

 ** _New Episodes every Monday afterward at 8PM EST_**

* * *

 ** _STARGATE UNITY: INFINITE DESTINIES_**

 _Summary: Working based on a mysterious message, everyone has to work together to reach a new destination that is apparently far outside of their reach. There, they hope to finally find the truth behind the meaning of life._

 ** _Will premier Thursday, June 29th, 2017_**

 ** _New Episodes every Thursday afterward at 8PM EST for 5 total episodes_**

* * *

 **STARGATE ATLANTIS: JOURNEYS FOR PEGASUS**

 ** _Written by Niko DelValle_**

 ** _Some ideas were borrowed from Joseph Mallozzi_**

* * *

 ** _PREVIOUSLY ON STARGATE ATLANTIS_**

The Wraith "Todd" informed the Atlantis Expedition of the existence of a ZPM-powered Hive Ship. Despite all of the ships dispatched, they were unable to prevent the ship from reaching Earth, and were forced to get help from Todd in the form of ZPMs they used to power a new technology on Atlantis. The Wormhole Drive. They were able to use the Wormhole Drive to travel to Earth, and with the help of Atlantis Recon 1, defeat the ZPM-powered Hive Ship with a nuke placed inside the ship after being transported through the Stargate. The fight forced Atlantis down to the planet's surface, where it was left in the San-Francisco Bay, with the power of their ZPMs almost completely depleted...

* * *

 **S06E01: Chronicles - Part I**

 **Year 2010**

* * *

John Sheppard stares out onto the water of the San Francisco Bay from a balcony on Atlantis. A beer is in his hand, and he takes a short and relaxed drink as he continues his lonely reverie. He continues to stare for a few short moments before yawning and sweeping his vision over to the Golden Gate Bridge.

"Bored?" Ronon Dex asks as he joins his friend on the balcony.

"Nope."

"Well I am."

"It's only been a month. You gotta relax. Have a beer! I brought a few…"

John gives the small cooler he brought with him a small kick in Ronon's direction.

"No thanks. It's been more than a month. I'm starting to get agitated."

"I can see that. But it's starting to look like we might be here a while, so you gotta-"

"If your leaders aren't going to let Atlantis go back to Pegasus, the least they could do is give us a way back."

"Yea, I know, you want to go and get back to fighting the Wraith. Everyone here understands that, okay? The Daedalus is still getting repairs. Once it's done, it'll come, and if you want to head back right away, I'm sure they'll be happy to take you."

"You sure they're going to let Teyla and me use the ship just for that?"

"Why not? You did die saving the planet after all. You're a hero! You should go spread that story around a little more. Hero worship can be pretty fun, you know? Coming back from the dead also happens to be pretty popular with my people. You should know that by now."

"Heh, I'd rather have one of your beers."

"Well, there you go. A plan of action. Now drink a beer and look at the bridge with me."

Ronon takes a beer and pops off the cap.

"It is pretty impressive. My people built a couple of things, but can't say they built anything like that…"

"You're people just didn't have as much style. They were all like you I bet. Very predictable. The ones we met certainly were. Uh… for the most part."

"Ha, you've got a point."

Both Ronon and John take a drink from their beers and stare out in silence for a few moments. They look at each other.

"You were lying before, weren't you?" Ronon asks.

"About what?"

"Not being bored."

"Okay, maybe I am bored. There's just nothing we can do about it right now. You just gotta-"

"…give McKay some time. I know. I've given him plenty of time. We're still here."

"Well, first of all, you gotta stop cutting me off like that. It's rude." Sheppard complains before changing tact. "Anyways, you know the situation. Using the Wormhole Drive drained power. The battle with the Wraith drained power. Hell, even landing drained power. The ZPMs are out of juice. There's nothing us non-geniuses can do about that. We're barely keeping the lights on around here, remember?"

"Hard to believe one of those things can last us so long and then we can eat it all away so quick."

"Well, you know what Rodney would say. Belief is not necessary."

"That's because it isn't." Doctor Rodney McKay says from down the hallway, looking up from his tablet is slight annoyance.

"What are you, bloody mary?" John asks.

"Ha ha, no. You didn't say my name seven times. But, I didn't come down here to chat."

"Huh. Is there a problem?" Ronon asks standing up straight abruptly. "Tell me there's a problem."

"What? No." McKay replies. "In fact, we've got the opposite of a problem. We've got a plan. Or, well, I've got a plan."

"Is a plan really the opposite of a problem?" Sheppard asks.

"This is no time for semantics, I've got a plan."

"You're going to need to clarify what kind of plan it is."

"What else would I walk all the way down here for? I've got a plan to get some new ZPMs."

"Is there somebody to shoot on the way?" Ronon wonders.

"Well, hopefully not, but… maybe?"

"Good enough for me. I'm in."

"Good to know. Are you two ready to beam up to the Daedalus? I already talked to Teyla. She'll join us up there."

"Hell yes." John replies throwing his bottle off the edge of the balcony. "I didn't know they had finished fixing it."

"Well, they did. Sorry for not keeping you in the loop on that one. I'll explain my plan once we get up there." He says, stepping toward them. He points toward the spot where Sheppard had just thrown his beer bottle from. "Good job polluting the planet by the way. That's not biodegradable, you know?"

"Well, sorry, it's just one bottle and we're in a hurry." John replies turning on his radio. "Daedalus, this is Sheppard, we're ready to beam."

"Got it. Beaming you up now." Came the response from Colonel Steven Caldwell. The three disappeared in a flash of light and appeared on the bridge. Teyla was present already, and gave Sheppard a nod.

"Good to see you all." Caldwell greeted them.

"Well, it's good to see you too." Sheppard replies. "I was starting to think the ship might be toast after that battle. Thought we might have to swing by to pick you up."

"Well, we're just fine, and now I gotta know what the plan is. McKay said something about getting new ZPMs for Atlantis?"

"We better not have to fly all the way to Pegasus and back McKay." Ronon warned.

"Well, sorry, but that's gonna be necessary."

"If I may ask, how did you manage to locate more new ZPMs in Pegasus from here Rodney?" Teyla inquires.

"I'm guessing it has something to do with why you requested Todd be brought on board." Caldwell says. "Not to mention all that equipment from your lab…"

"It does." Rodney says, not looking up as he continued to work on his tablet. "Woolsey did give you the green light on that by the way, right? I talked to him. Took a lot of convincing to get him on board with this whole thing, let me tell ya…"

"Yea, I already beamed him up from Area 51. The IOA was apparently not very happy about it. Zalenka too. He wasn't happy with being beamed up without warning."

"When are either of them happy about anything? That's why I didn't bother taking the time to explain in more detail to either of them. Luckily, they're pretty happy to accept any plan that gets Atlantis power again if I say we're in a hurry."

"Is Todd providing us with more ZPMs?" Teyla wonders. "If so, I question what you believe he will get out of it. If there is not significant benefit for him then we are taking a great risk by trusting any intelligence he might provide."

"What she means to say is… it's probably a trap."

"Well, he can get his freedom out of it, for one. But I didn't get this Intel from him anyways so we've got nothing to worry about. We just need his help." Rodney says. "But, uh, maybe we should continue this conversation in the briefing room."

"This should be good. Marks, take us out and get us on the way to Pegasus. Care to give him some more specific coordinates Doctor?" Caldwell wonders.

"Oh, yea, of course. Why don't you guys go ahead? I'll be right behind you." Rodney says going up to Major Marks and typing a bit on his computers, to Marks's obvious annoyance. "Okay, so we're going here… Got it?"

"Yea, I got it…"

* * *

 ** _Sometime later in the briefing room of the Daedalus…_**

* * *

"Okay Rodney, enough stalling. What's your brilliant plan?" Sheppard asks.

"Well, just like everyone else, you aren't going to like it." McKay says as he finished plugging his tablet into the board. "Radek, do you wanna take this one?"

"Do I wanna take this one?" Zalenka responds questioningly.

"Yea, you're right, what was I thinking?"

"I didn't say I wouldn't."

"Well, too late now. Blew your chance. Now I'm going to do it."

Zalenka curses annoyed in Czech as a response.

"Seriously, Rodney, what is the plan?" Sheppard inquires again.

"Okay, so you know how we've had so much trouble getting ZPMs over the years?" McKay asks.

"Yes, we are aware Rodney." Teyla answers calmly.

"Sorry, stupid question." Rodney admits as he changes tact. "Better question, remember Janus? Or, more specifically, his time machine?"

"Yea, we remember."

"Well, a long time ago, I read that mission file and I've been studying that machine in my off-time ever since."

"We have." Zalenka corrects him.

"Yea, yea… Anyways, while Zalenka still doesn't completely understand the device, working together we've managed to design a version for a bigger ship. Namely, the Daedalus."

"You want to go back in time to get more ZPMs?" Caldwell asks, clearly skeptical. "From who? The Ancients?"

"Well, no. No and yes." Rodney replies.

"Either way, time travel is generally a bad idea. Plus, this is sounding strangely familiar."

"While I admit that our work on the adaptation of the time drive to the Daedalus was inspired by the other Doctor McKay's work, this is not the same thing as that Parallel Reality Drive on the alternate Daedalus." Rodney explains. "We're moving through time, not other universes. Much safer."

"As far as I'm concerned, his other point still stands." Teyla states. "Do we not stand at risk of altering past events if we go back to contact the Ancestors? Is there even a guarantee they would provide us with what we need?"

"Well, no, that's why we're not going to talk with them." McKay says. "We also don't want to alter past events like you said. So, we won't be doing that either."

"Then what's your plan? Steal some?" Sheppard asks. "Cause that's also a bad plan."

"That's why we're not going to steal them either. Instead, we're going to go and find some that the Ancients were forced to leave behind during the war with the Wraith. That's why we need Todd." Rodney answers.

"Isn't that still stealing?"

"No. The Ancients left them behind to make sure their self-destruct went off."

"That doesn't explain why we need the wraith." Ronon comments.

"He was at the place I want to go ten-thousand years ago. I got the IOA to promise him his freedom if he can help me with this mission. More specifically, tell me when the Ancients leave, and what time the Wraith get there. That way, we can go in-between those two times." Rodney replies. "That way we just gotta walk in, take the ZPMs, and walk out. Also, because the Ancients destroyed this place, we can't alter any events by taking two of the ZPMs that are there and leaving the last one to the Ancients original plan of catastrophic overload. Simple."

"Sounds like it." Caldwell admits.

"Well, forgive me if I'm skeptical. These things never go as planned."

"But, they always end well, don't they?" Rodney asks. "Either way, we can't really pass this up. We need ZPMs for Atlantis. What happens if the ZPM runs out of the power necessary to maintain the cloak? What happens if the Wraith find another way to attack Earth?"

"Even if we do get these ZPMs, what's the chance your government lets us take the city back to Pegasus?" Teyla wonders. "As you said, the Wraith might attack Earth again, and it seems that the Wraith took out your planet's greatest defense during the attack. I highly doubt they will allow the expedition to return under these conditions."

"Yea, the things I've heard on that front… the chances aren't good." Caldwell comments.

"Pretty sure they're thinking of putting it on the moon." McKay replies.

"I'm sure they'll think about it." John says. "Either way, we could definitely really use those ZPMs. It's not like they'd give up on the Pegasus galaxy completely even if they did keep the city."

"Weren't you against this plan?" Ronon wonders.

"I still am. Time travel is a bad idea. I'm just saying I can see why they let it happen and it sounds like it's worth the risk. The Wraith do still know where Earth is, after all…" Sheppard says. "Plus, if you help with this, I'm sure they'll be even more willing to help kick the Wraith's asses."

"If you say so. Sounds like I might get to kill some Wraith, so I'm in anyways. Especially if it gets us back to Pegasus."

"I agree." Teyla says. "I will help, but I think Ronon and I agree that we will stay in Pegasus until your people have decided on Atlantis's fate. We have already been absent far too long."

"Well, these circumstances aren't the best, but I guess there's no real choice…" Sheppard says. "There is one thing I'm curious about. Why do we need the Daedalus for this? Why don't we just take the jumper?"

"What if we lose it? That's happened before." Rodney says. "We can't let the Wraith get their hands on that technology. We have no idea what they would do with it. Also, because the Wraith of ten thousand years ago haven't ever faced beaming technology, they don't have any countermeasures in place. If we get captured again, we can have the Daedalus beam us out."

"Okay, sounds like a plan then."

"Good! Then Radek and I will get to work on building the Time Travel Drive." Rodney says.

"You haven't built it yet?"

"We needed the ship to do that. We should be done by the time we get there. Sam also figured out how to convert the Asgard Shields to a cloak, so I'll be installing that little upgrade too."

"We, Rodney."

"Yes Radek… Geez, you can be really childish sometimes, you know that?"

"You have a go Doctor McKay." Colonel Caldwell says, standing up.

"Great! Let's go Zalenka."

"I am not a dog Rodney."

"I know, I know. You're just a lot like one."

The two scientists leave, continuing their usual bickering. As he leaves, Caldwell makes sure to add…

"The rest of you better settle in for the long haul."

"Ugh…" Ronon groans in annoyance.

"Guess we better head to the shooting range, eh Chewie?" Sheppard says patting him on the shoulder. "You're getting a little too antsy for my taste."

"Fine."

"I… will go locate my quarters and meditate." Teyla says.

* * *

 ** _Three weeks later…_**

* * *

"Did you run those calculations Radek?" Rodney asks as the duo sit in the engineering room of the Daedalus, which is flying in high orbit above a desolate planet below, dodging enormous asteroids as it goes. A large panel covers the new compartment where the Time Travel Drive is installed. McKay makes sure it is firmly in place before picking up his tablet. He is already in full combat gear and prepared to head out with the away team on the mission down to the planet, but feels he must make sure everything is working properly before leaving. "Yes, I sent them to your tablet."

Rodney examines them briefly.

"Good. Looks like we're ready to go." He got on the radio. "Bridge, this is Doctor McKay. We're ready. Just bring Todd in here so we can plot our course on the Time Travel Drive."

"You know, I'm really uncomfortable calling it a 'drive'." John responds.

"Well, then we can just call it a machine. Does that make you more comfortable? Seriously, don't worry about it. We've got this."

"Is this the new positive Rodney McKay?" Sheppard wonders. "Where's the doom and gloom?"

"It's my work John. It should never end in the worst case scenario when I have time to perfect it." Rodney answered. He adds a slightly whispered word that gets a small chuckle from Sheppard. "Mostly…"

"Todd is being sent down to engineering Doctor McKay." Caldwell says. "Make sure to tell me to activate the cloak before you turn that thing on. I don't want to appear in the middle of a Wraith fleet without a cloak."

"That reminds me! Make it very clear to Todd that if he betrays us again, I'll kill him." John says.

"I'm sure he knows but I'll tell him anyways. McKay out." McKay says. "Radek start the preliminary tests, would you?"

"Already on it."

"Oh, and make sure to test the-."

"Already done. It's fine."

"Got it."

The doors to engineering slid open, and Todd entered.

"You requested my assistance?" He asks.

"Don't mess with me. You already know why you're here, tell me when we're going." Rodney replies. "And Sheppard said he'd kill you if you betrayed us again. You can take those cuffs off by the way."

"I expected nothing less." Todd answers as his bonds are released and he is allowed entrance to engineering, with two guns from the soldiers pointing squarely at his back.

"Now, remember, we need to aim for the time period before your friends show up, but after the Ancients leave. Then we can come back and we'll let you go."

"I am aware. You should allow me to look over the designs for your device to make sure it works properly. I do not want us to get stuck somewhere we aren't supposed to be."

"It works. Don't worry about that, just give me what I need."

"Very well." Todd says, turning to the computers and entering the target time. "I am still coming with you, yes?"

"Yea, Sheppard would rather have you where he can see you."

"Understandable."

Todd finishes entering the data, and Rodney checks it before accepting the target with a nod.

"Hey, McKay, aren't we going to need space suits or something down there?" John asks as he looks out of the window on the bridge. "I don't see any trees."

"If we were going down there now maybe." McKay responds. "But we're going down there ten thousand years ago when there was a massive ocean and a mainland with plenty of vegetation."

"Where did it go?" Sheppard wonders.

"Remember the whole sun thing from the future? It's happening in this solar system too. The Ancients really know how to pick em." Rodney says. "Anyways, we're ready to go, you should engage the cloak now Colonel."

"That's not up to me Rodney."

"I wasn't talking to you. I was talking to Caldwell."

"The cloak's been engaged Doctor McKay." Caldwell assures him. "You may begin when ready."

"Beginning."

Rodney puts his tablet down and types a command into his computer before hitting the enter key. The buzzing noise previously sitting in the background of the room's soundscape suddenly grows to a din, and a beeping noise begins to pulse on and off. If one were to see the outside of the ship, it seemed that the Daedalus had just dived into a perfectly clear ocean and was spreading the water. Everything around them shifted. The planet was suddenly filled with water and the sunlight was a lot less intense.

"It looks like it worked. Scan for lifesigns Bishop." Caldwell ordered.

"I've got nothing on sensors, sir." He responded.

"Ships?"

"Nothing. Except for something on the planet's surface. It's got similar readings to Atlantis…"

"Sounds like what we're looking for." Caldwell said. "You should get moving Sheppard. We don't know how long we're going to be alone here."

John leaves the bridge at a run.

"Rodney, get down to the 302 bay now."

"Already on my way." The doctor responds.

"Todd's with you?"

"Yea."

"Ask him how much time we have before the Wraith show up."

Rodney asks. He then tells Sheppard.

"Todd says he can't know exactly when, but he thinks we have about twenty minutes."

"Hopefully that's enough time to get the ZPMs and then return to the jumper."

"I'm guessing that's not enough time to get back to the Daedalus." Caldwell says joining the conversation. "I'm going to hide the ship beyond sensor range so you can come out there to meet us."

"Sounds good." John says as he enters the 302 bay and boards a jumper they brought along with them. Ronon and Teyla are already on board as he takes the controls. Rodney and Todd arrive soon after, though Ronon makes sure he trains his gun on the Wraith the second he comes into view. "See you when we get back. Make sure to keep the lights on for us."

"Wouldn't think of turning them off. Good luck."

"Appreciate it. We're taking off now."

At John's command, the small ship leaves the floor of the Daedalus 302 bay and shoots out into space where it immediately cloaks. He then turns it towards the planet, directing it toward the Ancient outpost. The screens pop up a 3D-model of where they're going.

"Isn't that…?" John wonders.

"It does look incredibly similar to the city of the ancestors." Teyla comments.

"It's not Atlantis." Rodney says without looking up from his tablet. "We're near the turning point of the war against the Wraith. The Ancients are just starting to lose, so they want to build another city-ship to fight them with."

"They are unsuccessful." Todd comments. "Our scouts found the location of this base from data we lifted from one of their ships. Once we found out, we had to stop them. Once we arrived and detected no lifesigns however, we decided to investigate. It was a trap. Soon after we arrived, the timed self-destruct went off and destroyed nearly a dozen of our ships."

"Looks like you survived." John comments.

"Yes, I was in command of most of the hive ships that were destroyed. As such, I was in the rear and was unaffected by the explosion."

"How big an explosion is this exactly?" Ronon wonders.

"Really big." McKay answers. "These are ZPMs that the ancients decided to overload, remember? I still don't quite understand how they did it, but if you did figure it out, you could make a bomb capable of decimating the surface of a whole planet and anything in orbit. Where do you think all of those asteroids that were in the present came from?"

"That is what happened." Todd confirms.

"The planet does look a bit bigger now. Can't really tell." John replies.

"You wouldn't be able to with the naked eye as far as I know…" McKay responds.

"Anyways, we're getting close. I'll put us down in their jumper bay and we can run down to the power room. I'd prefer to get out of range of that self-destruct as quickly as possible."

"Run away from the big explosion. No one's ever thought of that…" Rodney trails off as he stands up. The jumper comes in over the central spire and descends into the jumper bay where the rear door opens up.

"Okay everybody, let's make this quick." John says.

"You stay ahead of us." Ronon orders Todd.

"Very well, though I do not know exactly where I am going."

"Just follow me." McKay says pulling out his lifesigns detector as he descends the ramp. Todd comes next, followed by the rest of the team. As they move throughout the incomplete city, the fact that it is not yet finished becomes more and more clear to them. Many walls are still open to the outside and almost all of the windows are yet to be installed, making the myriad corridors very drafty. The city also houses little in the way of décor or personality. Regardless, it doesn't take the team long to reach the power room. McKay makes quick work of ejecting two of the ZPMs.

"What's the countdown on that self-destruct Rodney?" John asks. "And why isn't there an alarm?"

"Looks like most of the city hasn't had the intercoms installed yet." Rodney answers as he heads to a computer. "It also looks like the self-destruct still has a bit over twenty minutes left. We should be fine."

"Hm…" Todd says.

"What?" Ronon asks aggressively.

"We did not hit my target time precisely."

"What do you mean?" Rodney asks as he stuffs the ZPMs into his bag.

"The self-destruct should still have thirty minutes according to my calculations." Todd says.

"Wait, so you mean…?" John asks.

"Sheppard! Two dozen Wraith Hive Ships just dropped out of hyperspace in orbit!" Colonel Caldwell says.

"Oh crap. Rodney, we gotta move!"

"I'm done!"

"Everybody back to the jumper!"

Before they can start running, Ronon shoves his gun into Todd's chest and pushes him against the wall before yelling an accusation.

"You did this on purpose, didn't you!?"

"No, of course not. I have no desire to change the past."

"Oh really? Why not?" John wonders. "I bet circumstances would really improve for you if your hive ships weren't destroyed. If they captured us, they would avoid the self-destruct, right?"

"I may not be completely satisfied with current events, but I guarantee you that not losing a few Hive Ships would do very little to change my standing with the Wraith when we exited hibernation. Besides, why would I want to change his life? My life is the only one that matters to me."

"I don't believe you."

"We do not have time for this." Teyla urges.

"She's right Ronon. Bring Todd with us, we can hash this out later." John says urgently. "Daedalus, we've gotta get our hands on a new jumper."

"What's going on down there?" Caldwell asks.

"Problems." Is Sheppard's only response. Rodney has more.

"Look, whatever you do, do not let the Wraith see that ship and don't use the Asgard beam more than once."

"Why not?" Caldwell wonders.

"What do you think would happen if the Wraith had countermeasures for the Asgard beams before we even met them? What would happen if they recognized us the first time they saw us? I personally don't want to find out."

"Fine. We'll play it your way."

"This is Sheppard's team out." John interrupted to get back to the matter at hand.

"I'll take the lead this time." Todd says with an off-putting grin as the group takes off. Suddenly, the city rocks with the impact of weapons fire. "They have detected our lifesigns! Their first target will be the central spire where your ship is!"

"Then hurry up!"

"It's too late! Stop!" Rodney calls out. The group halts.

"What do you mean?" Sheppard asks.

"There are no shields on right now! The jumper bay has almost definitely already been destroyed!"

"Then what do we do?"

"Gimme a second…!"

"Rodney! We don't have a second!" Another salvo of weapons fire rocked the city as the group struggled to keep their footing.

"Are there not additional jumpers elsewhere in the city? The underwater bay, maybe?" Teyla inquires desperately. Rodney begins snapping as he looks up with a grin.

"Yes! You're right! The underwater bay should have some extra jumpers, but there's no way we can make it…" Rodney says.

"How so?"

"The entire area is flooded. There are no windows yet, the entire thing is still under construction. We'd drown long before we reached it. We're doomed."

"Focus!" John urges grabbing McKay by the shoulders. "Does this thing have shields and weapons? We've gotta at least fight back. Though, I'd prefer to live."

"Yea, that would've been the Ancients first priority." He replies. "Wait… the Star Drive…!"

"You want me to fly the city?" John wonders.

"Yea! If you can get us of the surface, all of the water will run out of the jumper bay and we should be able to get down there." Rodney replies. "I doubt the city is spaceworthy yet though. Especially because of the damage from the Wraith ships…"

"It doesn't need to be spaceworthy as long as it can get off of the ground, right?"

"Right. I just need to plug back in the ZPMs long enough for you to complete the initial launch. Once we're in the air, we can pull the ZPMs again, run down to the jumper bay, and then we swing back around somewhere outside to pick you up."

"Good. We have a plan. I'll get to the chair room, you guys get moving. Except for you Todd, you're coming with me."

Todd gives a slight nod in acknowledgement.

"Very well." Teyla says as John flips around and starts running, quickly followed by Todd. "Let's hurry."

Teyla and Ronon also take off.

"Hurry up McKay!" Ronon calls back.

"I'm hurrying!" He calls back as he takes off at a run. He makes sure to complain under his breath as he does so. "Always with the running…"

The trip to the power room is constantly disturbed by the Wraith ship weapons fire from orbit hitting the city. Through the unfinished windows exposed to the open outside air, the team can see spires being hit by blue bolts of light. Explosions rip through these towers as several sections collapse under the intense bombardment. Luckily, they make it in decent time, and it doesn't take long for McKay to plug-in and reinitialize the two ZPMs.

"John! You're good to go!" Rodney yells into his radio. The response is almost instantaneous as the city begins shaking with the activation of the engines.

"I'm activating the shield!" John calls back from his place in the chair room. "Get to the jumper quick, we're not going to be able to hold it for long!"

Suddenly, Todd hides behind the side of the door to the chair room.

"Give me your weapon!" He urges. "They're here."

"What?" John wonders.

"Some of those explosions before were darts. We've been boarded. Now, give me your weapon!"

Reluctantly, John throws Todd his sidearm, which the Wraith immediately takes before opening fire onto the hallway outside where a small group of Wraith soldiers wait. They immediately return fire as the one at the forefront is taken down by Todd's gunfire. The sidearm quickly runs out of bullets.

"I will be back. I must retrieve a superior weapon…"

"They'll recognize you!"

"I will not allow them time to report that information."

"Damn it!" John curses as the city starts to lift off from the water. He can only hear the sounds of fighting through the open doorway as Todd slides into grabbing a Wraith stunner from the ground and shooting at the other Wraith. "Rodney, the city is high enough now! Get those ZPMs and run back to the jumper bay!"

"Working on it! So don't you dare say 'work faster'!" Rodney replies

"I wasn't going to."

"Sure you weren't."

"It doesn't matter, just get moving!"

"We're heading to the jumper bay now!"

"Good, I'm putting the city on autopilot. Pick us up towards the middle of the central spire! And I hate to repeat myself, but hurry up because our power isn't going to last long."

"I'm aware of that!"

"We are moving as quickly as we can John." Teyla chips in.

"Well, we'll meet you there." John says running to grab his pistol and holster it. He then emerges from the door with his P90 blazing, mowing down the remaining Wraith. "We gotta move. We don't want to miss our ride. We're going to meet them around the middle of the central spire."

"Yes, but first things first." Todd replies. He grabs a rifle-length Wraith stunner and executes any remaining alive. "Now we can do that."

"It really looks like you care about your people." Sheppard says sarcastically.

"They died a very long time ago." The Wraith counters. "I'll lead the way."

"So, I guess this means you don't really want to change the past?"

"The way I understand it, changing the past would mean that I would lose my place in the future. It wouldn't be me that benefits, but the version of me that is here. That is not a desirable outcome."

"I guess I can count on you to be selfish."

Todd chuckles as the head into a tunnel. It doesn't take them long to reach their destination and head out onto a balcony. John quickly feeds their exact location to Rodney and the others, who had reached the underwater bay and retrieved a jumper.

"We will be there soon John." Teyla assures him.

"How do you intend to board the vessel?" Todd asks. "If they approach too close, they will be hit."

"I'll jump."

"You cannot make a jump of the necessary distance. Only I can."

"You're still strong enough?"

"Luckily, I fed very recently when your people captured me. I will be fine."

"Good to know…"

"That still does not solve your problem."

"And I suppose you've got a solution?"

Todd chuckles again.

"Yes, John Sheppard, I do. I can throw you."

"Fat chance of that happening." John replies. The jumper pulls up as he talks and the rear hatch descends. It is quite a long distance between the railing of the balcony and the small vessel. "Can't you get any closer!?"

"No! We'll slam right into the city!" McKay calls back.

"I can leave you behind if you wish." Todd tells him.

"Ah, screw it, just do it…"

Todd does not hesitate and grabs Sheppard by the belt, tossing him over toward the ship. Ronon and Teyla catch his extended hands and pull him up.

"Can we just leave him?" Ronon asks as they pull him up.

"No, as much as I would like." John says as he heads for the front to take the pilots seat.

"I've got it." Rodney assures him, but John makes him move anyways. Todd does not take long to board and the group shoots upwards with cloak activated. The city is high enough that space is not a long distance away. But, they barely get any distance before the shield on the city fails, and the Wraith bombardment continues. John immediately starts swerving to avoid the weapons fire.

"What happens if the city is destroyed? Will the self-destruct still activate?" Teyla wonders.

"Yea, don't worry about it. The catastrophic overload has been programmed directly into the ZPM. Even if the city is destroyed, that thing will still go off. Don't worry about changing history or anything."

"Isn't it already too late for that?" Ronon wonders.

"Uh… I don't think so."

"That's reassuring."

"Well, as long as the Todd in this time doesn't have any reason to change his future actions, we'll be okay."

"Are you sure they can't see us?" John complains from the front. "I'm having trouble evading all of this."

"Just get out of reach of the city!"

"I'm trying Rodney! I keep getting cut-"

He is interrupted as the jumper violently shakes thanks to an impact from a Wraith weapon. They are in space at that point, but the shot had struck them almost directly, taking out their right drive pod and disabling the cloak. The shaking sends everyone inside flying around the compartment. John's head smacks into the console, Rodney flys into a wall, Teyla bounces off of the ceiling, and Ronon impacts the rear hatch. Todd is the only one that manages to hold on while all of the others except Ronon fall unconscious. The gruff man attempts to move, but is unable to stand.

"Well, it seems we are in quite the predicament…"

The radio turns on.

"Sheppard! This is Caldwell! We're reading that your cloak is gone! Should we beam you? Respond!"

"Hm…" Todd says.

"Hey, whatever you're thinking, if you do it… I'll kill you." Ronon says, trying to move unsuccessfully. The Wraith moves to the front compartment and retrieves Sheppard's radio. "Tell them to beam us back!"

"No, I don't think I will." Todd replies.

"I knew you were betraying us!"

"In fact, I wasn't before. But… this situation presents an interesting opportunity for me, you see. I would be foolish to pass it up."

"If you don't respond we will beam you now!" Caldwell says over the radio.

"Now, you will tell him to not beam us." Todd says bending down in front of Ronon.

"I'll kill you before that happens!" Ronon threatens.

"No, I don't think so. You will tell him that Doctor McKay is repairing the jumper and said that because of something you don't understand, beaming us from anywhere in this solar system would kill us all. If you do, I'll make sure you all come out of this situation alive. If you don't, I will kill all your friends. You know that isn't an empty threat."

Ronon remains silent for a moment as Todd depresses the activation button and puts the radio Ronon's lips. The Wraith extends his hand a bit towards Teyla as he waits.

"This is Ronon. Don't beam us… McKay said that doing that in this solar system would kill us. I don't understand why. He's… fixing the jumper. Ronon out."

Todd chuckles as he deactivates the radio before a response.

"Good. Good." He says as he stands up, and before Ronon can issue any further death threats, Todd shoots him with the Wraith stunner. Todd sits in the forward compartment to wait patiently as one of the Wraith hive ships approaches to retrieve the damaged jumper…

* * *

 ** _STARGATE ATLANTIS: JOURNEYS FOR PEGASUS_**

 ** _A Fan-Written Conclusion to Stargate: Atlantis_**

 ** _Stargate initially conceived by…_**

 ** _Roland Emmerich_**

 ** _Dean Devlin_**

 ** _Television Show originally created by…_**

 ** _Brad Wright_**

 ** _Robert C. Cooper_**

 ** _Writing ideas gleaned from…_**

 ** _Joseph Mallozzi_**

 ** _Written by…_**

 ** _Niko DelValle_**

* * *

 ** _All copyrights belong to their respective owners._**

* * *

 ** _NEXT TIME ON STARGATE ATLANTIS_**

Atlantis Recon 1 has been captured by the Wraith of ten-thousand years in the past. Due to a betrayal by Todd, they have no hope of being rescued by the nearby Daedalus. Therefore, it is all up to them to break themselves out, and bring to a stop whatever devious plan Todd has in store… not to mention return to their own time without dire consequences.


	2. S06E02: Chronicles - Part II

_**Sorry this was late guys! I had a really tiring day and accidentally fell asleep. I had to rush myself to get this finished up, so I apologize for any mistakes I may have made while writing this. I'll correct it later if necessary.**_

 _ **Sorry for the tense switch by the way. I wanted to try and write this story in the present tense as a challenge to myself, but I am simply too used to writing in the past tense when it comes to fiction. I keep slipping back into it as a write and having to make the corrections is pretty annoying. So I'm just going to stick with past tense from now on. Have fun reading!**_

* * *

 **STARGATE ATLANTIS: JOURNEYS FOR PEGASUS**

 _ **Written by Niko DelValle**_

 _ **Some ideas were borrowed from Joseph Mallozzi**_

* * *

 _ **PREVIOUSLY ON STARGATE ATLANTIS**_

SHEPPARD: "Using the Wormhole Drive drained power. The battle with the Wraith drained power. Hell, even landing drained power. The ZPMs are out of juice."

RONON: "It's been more than a month. I'm starting to get agitated."

MCKAY: "I've got a plan to get some new ZPMs."

MCKAY: "…remember Janus? Or, more specifically, his time machine?"

MCKAY: "…while Zalenka still doesn't completely understand the device, working together we've managed to design a version for a bigger ship. Namely, the Daedalus."

CALDWELL: "You want to go back in time to get more ZPMs?"

TEYLA: "Do we not stand at risk of altering past events if we go back to contact the Ancestors? Is there even a guarantee they would provide us with what we need?"

MCKAY: "That's why we're not going to steal them either. Instead, we're going to go and find some that the Ancients were forced to leave behind during the war with the Wraith. That's why we need Todd."

MCKAY: "He was at the place I want to go ten-thousand years ago."

MCKAY: "…we just gotta walk in, take the ZPMs, and walk out. Also, because the Ancients destroyed this place, we can't alter any events by taking two of the ZPMs that are there and leaving the last one to the Ancients original plan of catastrophic overload."

 _The team enters the city-ship abandoned by the Ancients in a cloaked puddle jumper and retrieves the ZPMs. Just as they grab them, they realize that there are twenty minutes left on the self-destruct timer._

TODD: "The self-destruct should still have thirty minutes according to my calculations."

CALDWELL: "Sheppard! Two dozen Wraith Hive Ships just dropped out of hyperspace in orbit!"

TODD: "They have detected our lifesigns! Their first target will be the central spire where your ship is!"

MCKAY: "The underwater bay should have some extra jumpers, but there's no way we can make it…"

MCKAY: "The entire area is flooded. There are no windows yet, the entire thing is still under construction."

SHEPPARD: "You want me to fly the city?"

MCKAY: "Yea! If you can get us off the surface, all of the water will run out of the jumper bay and we should be able to get down there."

 _The cloaked Puddle Jumper the team is travelling in is hit by the Wraith Hive Ship while they're trying to escape, and they are all knocked out except for Todd and Ronon. Ronon is injured and unable to move._

CALDWELL: "Sheppard! This is Caldwell! We're reading that your cloak is gone! Should we beam you? Respond!"

TODD: "You will tell him that Doctor McKay is repairing the jumper and said that because of something you don't understand, beaming us from anywhere in this solar system would kill us all. If you don't, I will kill all your friends."

RONON: "This is Ronon. Don't beam us… McKay said that doing that in this solar system would kill us. I don't understand why. He's… fixing the jumper. Ronon out."

 _Todd goes to sit in the forward section of the jumper and chuckles as he waits for the Wraith Hive Ship to pick them up._

* * *

 **S06E02: Chronicles - Part II**

 **Year 7988 BC**

* * *

The crew of the Daedalus on the bridge were in a panic as the ship headed back into beaming range of the planet. They could detect the damaged jumper, but thanks to Ronon's warning, were unable to do anything to interfere.

"Sir, the jumper has been retrieved by one of the ships that was at the back of the battle line." Major Marks said. "The Wraith have also stopped their bombardment of the city now that the shields are down. They are dispatching darts to check it out, though it seems they are waiting for it to fall back to the surface first…"

"Shouldn't we help them, sir?" Bishop wondered. "Sheppard's team, I mean…"

"You heard what Ronon said. If Doctor McKay says we can't beam them, then we've got no choice but to wait." Caldwell said, placing his chin upon his fits. "We don't know what would happen if we tried to interfere directly, and even if we did we're outnumbered. They're on their own. But they've probably been in worse situations then this. I'm sure if we wait, they can take care of this on their own. We just have to be patient…"

"Yes sir…" The man trailed off in response.

"Sir, I don't mean to question you, but didn't Ronon's communication sound a little… coerced?" Major Marks asked. "Also, why didn't Doctor McKay just contact us himself? Is he really that busy?"

"So, you noticed it too?" Caldwell asked, sitting up straight and turning to look at Marks. "I agree, but I don't see what we can do about it. Considering the hit that ship took, it could've sounded that way just because he was delirious from any injuries he took… And maybe Doctor McKay is really that busy…"

"Yes sir. I understand completely."

"Stay ready just in-case. If I feel the situation has gotten too desperate, we're going to do it anyways. I just want to give them a chance first."

Major Marks nodded and got back to work.

"I just hope I'm making the right choice…" Caldwell trailed off.

* * *

 _ **A SHORT WHILE LATER, ON BOARD A WRAITH HIVE SHIP…**_

* * *

Todd the Wraith was escorted through the corridors of the Hive Ship at gunpoint. Atlantis Recon 1 was nowhere to be seen as he was taken right into the throne chamber where his old queen waited. His old queen… and his old self. A look of shock crossed both of their faces as their eyes fell onto the familiar Todd, who went to the center of the room with a large grin on his face. The past version of Todd cleared his shock quickly, as the future Todd had expected.

"What is the meaning of this?" The Queen wondered, waving the Wraith warrior drones away.

"Please, my Queen, just because this one bears an uncanny resemblance to myself means nothing…" The past Todd said.

"You don't need the charade. We both know who's really in charge here." The future Todd said with a chuckle.

"He speaks like you too?" Then Queen said. "And he knows…"

"Why were you helping the humans!?" The past Todd asked. He walked aggressively toward the future Todd, who grinned… as things were going exactly as he predicted. "A Wraith taking the side of food… it doesn't make sense!"

"So young, and so foolish." Todd said in reply. The past Todd reached out a hand and grabbed the future Todd by the throat.

"Your mind… it is mine…" The past Todd said. Suddenly, he grabbed future Todd's right hand with his left as it went in for a strike with a hidden knife. "And… you are the same as I am in that way too…"

"Ah, but there is a key way in which we are different." The future Todd replied, not letting his grin lapse for even a moment.

"And what is that?"

Suddenly, the entire ship is rocked as the city-ship below explodes in an enormous resounding fireball. The shaking distracts the past version of Todd just long enough for the future version to take his knife back. The noise of the stab resounds throughout the room. Future Todd dropped his hand from the knife in past Todd's chest, whose eyes went wide as he dropped to the ground. The past Todd looked up at his future self from the ground as a pool of blood spread.

"You weren't prepared for the real plan." The future Todd said. He turned to the Queen. "I am in charge now. Do you understand?"

They looked at each other for a long moment.

"Yes…" She replied. The future Todd turned back to look at the past Todd. He gave it a long moment, before stomping on the knife, driving it deeper into his chest and finishing the job. The past Todd died with a gasp.

"Now, have someone get rid of him, and deal with the mess outside. I have things I must attend to."

Todd left his past selves corpse and his past selves Queen behind in the room as he departed, hands crossed behind his back. He retrieved the gear of Sheppard's team and then found his way to the detention cells. There, the team was just waking up, except for Ronon who remained unconscious due to clear loss of blood despite bandages that had been wrapped around his wounds.

"Oh no, this is a Hive Ship…" Rodney complained. John spotted Todd coming quickly.

"Todd! You betrayed us, again!" He yelled annoyed.

"Are you really surprised?" Todd wondered.

"Well, no, but that doesn't make me any less annoyed."

"Well, maybe this will."

Todd opened the cell and gave them back their gear. Including their weapons.

"You are free to have your ship beam you away."

"He has to come with us! He'll screw up time!"

"But, I have to stay Doctor McKay." Todd said with a grin. "If I didn't, you would be removing me as a factor. We have no idea what that might cause, correct?"

"What did you do?" Rodney wonders. "Where is the other version of you?"

"I killed him."

"But, shouldn't you have dis-? Oh. Oh no… I understand."

"What is it Rodney?" Teyla wondered.

"We theorized that if someone went back and killed someone off, the target would just disappear as the timeline shifted and a parallel universe was created. Well, that or they would just be erased altogether. One of the two…" Rodney explained. "But, anyways, since we're in the past we must be somehow either vulnerable to changes in the timeline or shielded from a grandfather paradox disappearance effect. So we ended up in the same parallel universe that Todd did."

"So, basically, time doesn't make sense." John replied.

"Of course it makes sense. Everything has rules, we just haven't figured them all out yet."

"I don't think it matters." Teyla replied crouching down next to Ronon. "He needs medical attention."

"Well I'm not leaving until I make good on my promise." John said raising his P90. Todd put his hands up with a small chuckle.

"No! You can't!" McKay called grabbing his shoulder. "He's the only one here now. If we don't leave him alone, it could irreparably damage the timeline."

"Wouldn't leaving him here do the same?" Teyla asked.

"She's got a point." John said.

"I only plan to change a few tiny things." Todd assured them. "Believe me, I could care less about your planet as long as I'm the most powerful among my kind. With knowledge of the future, I can change my standing.

"Besides, wouldn't that help you spread your cure once it is finished? If I am the most powerful Wraith, I can force all of the others to adopt it."

"Looks like he's got a point too." McKay said.

"I made a deal with your injured companion. I said that if he told your ship not to beam you, I would make sure you all lived. Have I not lived up to my end of that deal?" Todd asked.

"Well… sure… but you shouldn't have crossed us to begin with." John responded.

"You have your ZPMs and now when you get back to the future, you should have a powerful advantage as long as we continue to work together. If you don't kill me, then I will try to have as little effect on the timeline as possible, just enough that I end up in charge. Is that not preferable?"

"Hey, Sheppard, I don't think we have much of a choice other than to trust him…" McKay said.

"Fine." John said, lowering his weapon. "But you know what happens if you betray us again Todd."

"Of course."

"I told you this was a bad plan…" Sheppard said, grabbing his radio. "Daedalus, this is Sheppard."

"It's good to hear from you. We were starting to fear the worst." Caldwell responded. "We're here to render any assistance you need. Maybe I can offer a distraction so you can escape? You know, since we can't beam you…"

"You can beam us. Ronon was forced to say that by Todd."

"Sounds like a long story."

"Yea, and we'll tell you all about it once we're on board."

"Your Wraith friend's locator beacon isn't showing up. I'm assuming he's dead?"

"No. But you don't need to worry about him anyways. Just beam us. Make sure Ronon gets to the infirmary, he's in pretty bad shape."

"Alright, on it."

The team disappeared in a flash of light as Todd turned and left. John, McKay, and Teyla arrived on board the bridge.

"Hey, thanks for the save." John said. "Mission was mostly successful. We've got the ZPMs. But, we'll save the debrief for later. Let's get back to the future before something else bad happens."

"Sounds good to me." Caldwell said. "Marks, activate the Time Travel Drive and get us back home."

"Yes sir." He replied.

At first, everything worked fine, and the ship travelled back to the present. Only, the second they got there, they were being bombarded from all sides by Wraith Hive Ships. Sparks shot across the bridge and pipes exploded to release clouds of steam.

"Get the shields online now!" Caldwell suddenly shouted as the alarms went off. "All crew, get to your battlestations! Damage report! How are the Asgard weapons?"

"They're offline along with the hyperdrive!" Marks yelled back. "They were targeted in the initial attack! I managed to switch the cloak to a shield before we lost any other major systems, but we've taken a lot of hull damage."

"Return fire with all railguns and missiles then! We're not going down without a fight!"

"Yes sir!"

"Sir, I'm getting familiar readings." Bishop said. "At least one of those ships is powered by a ZPM."

"How did they know we were here!? Our cloak was online!" Rodney wondered confused. "Unless… they were already here waiting for us."

"Looks like Todd reneged on his deal. So much for being trustworthy." John said.

"He must've marked our position when we jumped forward in time." Rodney said. "He tracked the energy burst and then surrounded our position with ships when he knew we would be here."

"There's no way we can compete with this fleet. There are too many ships and they got the jump on us. Any suggestions?" Caldwell asked. "I could try to jump to hyperspace, but we're surrounded. I'd need to open up a path, and without Asgard weapons…"

"What about the Time Travel Drive?" Teyla wondered. "Can we not escape to a different time?"

"No. We can't activate that when we're under attack." McKay responded. "When we activate the Time Travel Drive, we become very sensitive to energy variations in the immediate vicinity of the ship. If we activated the time travel drive when being hit by a weapon, it would carry foreign exotic particles through time with us."

"In English?" Caldwell asked.

"The ship would explode. That's not a percentage chance either, it's guaranteed. One-hundred percent."

"Then hyperspace it is. Can you get our ZPMs connected to help us get out of this situation?"

"Yea! Good plan!" McKay replied. He checked his bags for the ZPMs, but they were gone. Replaced with rocks that had simulated their weight. "Oh no! Damn it! Todd took them!"

"Of course he did. Crap." John commented. "But how were we going to escape into hyperspace with that anyways? You said we're trapped here, right?"

"That's right. So ZPMs or no ZPMs, now might be a time for a brilliant plan Doctor McKay!"

"Yep, that's me! Brilliance on demand!" McKay said crouching over his tablet.

"You know, there is one way we escaped from the Wraith before…" John said. "But it was with Atlantis. I think it might work here."

"I'm all ears." Rodney replied.

"Remember when we detonated that nuke above Atlantis and activated the cloak?"

"To make it look like Atlantis self-destructed… yea… So you want to detonate a number of nukes around us with the shield active, then switch to cloak to confuse them not firing, then we travel back in time."

"Uh… yea. More or less." John said.

"That could work. But we need to do it now, and also we need to move at least a bit first… If we travel back in time now we'll be in the same exact position we were when we left. We don't want to risk ending up inside of our own ship. That could cause problems."

"Why would we go back there?" Teyla wondered.

"To kill Todd of course." John replied.

"No, to rescue him actually." Rodney said. "I'm going to set up the Time Travel Drive to take us back to when we were on the jumper. We can board the ship and stop Todd from killing his past self. Then, there shouldn't be any interference with the timeline at all, and we can come back totally fine."

"I can still kill the future version, right?"

"I guess, but then how are we going to disseminate that cure?"

"This isn't really the time." Caldwell interrupted as another salvo shook the ship. The shaking was much more tolerable with the shield online. "You should go reprogram the Time Travel Drive Doctor McKay."

"Oh, yea, of course. I'm on my way. I'll make the calculations and send you the coordinates for those nukes."

Rodney left the bridge.

"You know, Todd did allow us to live." Teyla said. "Does it really make sense that he would plan this attack when he could've simply had us killed while we were unconscious?"

"You've got a point…" Sheppard admitted. "Also, I feel like he would've contacted us when we got here. He may not have been behind this. I guess we'll never find out since we won't be spending any time here."

"We can ask him of his plans when we take him prisoner again." She replied. "Though, I do have to wonder what the result of Todd's actions are. If the Wraith are here in such force, then our galaxy… and your planet…"

"I don't want to think about it." Sheppard cut her off and turned on his radio. "McKay, how's this plan of yours going?"

"It's almost ready! Just give me a couple more seconds!"

The ship takes another salvo of fire. Another shower of sparks cascades across the bridge as a fire starts in the rear.

"Shields are down to twenty percent!" Marks yells.

"Transfer all power from secondary systems and give McKay the time he needs!"

"On it sir!"

"Rodney, if you don't hurry up we're not going to have power left for the cloak or to bear the force of the nukes!" Sheppard yelled.

"I sent my calculations over to Marks and the Time Travel Drive is ready to go!" Rodney called back.

"Launch those nukes as soon as you are ready Marks!" Caldwell yelled.

"Ordinance is away!" Marks called back. "Everyone cover your eyes!"

They all did as suggested as the nuclear weapons detonated outside of the ship. The light shone even through their shut eyes.

"Transition to the cloak on my mark! Make sure to move the ship once we transition so we don't get hit by any follow-up volleys while the Time Travel Drive is charging! And, of course, so we don't end up in the same spot as ourselves…" Rodney said over the radio. "We've just got to wait until the radiation drops to levels that won't penetrate the hull!"

"Get your finger on that button Marks!" Caldwell ordered.

"Already there, sir!" He responded. Several seconds passed and the light began to fade.

"Mark!" McKay shouted. Marks immediately switched the ship to cloak.

"Get the ship moving to a safer space before they open fire again!" Caldwell ordered.

"We're on the move!" Marks replied.

"Activate the Time Travel Drive!" Rodney called.

"Already done!"

It doesn't take long for the Time Travel Drive to finish charging, and the Wraith ships to disappear from view.

"Good job Doctor McKay. Your plan worked." Caldwell said.

"Hey, it was _my_ plan." John complained. "Oh god. I just sounded like McKay, didn't I? Pretend I didn't say that."

"Sorry but we don't have the time for banter." Rodney replied. "You're going to need to beam us aboard since we don't have a jumper anymore."

"I thought I was only supposed to use it once." Caldwell reminded him.

"We haven't used it yet. The version of us here is still being picked up by the jumper, remember?"

"Ah…"

"How about once we're on board Rodney?" Sheppard wondered.

"Our first priority should be getting those ZPMs back. We might even be able to kill two birds with one stone if they escorted Todd along with us." Rodney replied.

"What about the us that's here? I don't think shooting bullets their way is going to be very diplomatic with their Daedalus."

"Then we'll need to get to the armory first and pick up some stunners. If we give them some too, then we should be able to storm the throne chamber together and get our Todd back. Assuming of course we didn't capture him already."

"Aren't those ZPMs rightfully theirs?" Teyla wondered.

"Speaking of, if we both go back to the present, won't there be two of us now?" Sheppard wondered.

"Look, it's very complicated, but as long as we talk to the other me and make it clear that we go back to the same exact time then there won't be a problem. The universe can't account for two versions of us arriving at the same time, so it should split us into our own distinct timelines." Rodney replied. "As for the ZPMs, I don't know… maybe we can share?"

"No. If we do that, Atlantis won't be able to take off. We need at least two ZPMs, right?" Sheppard replied.

"Yea, that's right. So we'll just have to beam them back to the ship and they'll have to find their own." Rodney answered. "If it makes you feel any better Teyla, we're helping them break out of captivity a little early."

"We're just going to have to lie to them. We'll tell them that the ZPMs are still stored with their gear. They can go and search by themselves once we stop Todd, but we'll already be long gone."

"I do not like it, but I understand why it's necessary." Teyla said.

"Are you all ready to go then?" Caldwell wondered.

"Not yet. I need to switch our subcutaneous transmitters to a different broadcast frequency." Rodney answered. "Also, for external communication, we've gotta switch that frequency up too."

"Why?" Caldwell wondered.

"We don't want to conflict with the other Daedalus floating around here." He answered.

"This is all making my head hurt, but if you say so Doctor McKay…"

"Anyways, once we beam in there, you've gotta be prepared to break that one beam limit. If we can't make it back to the dart bay it'll be our only way out."

"But what about the Wraith figuring out the jamming codes?" Caldwell asked.

"We have to risk it to get Todd out of there. Besides, last time we beamed nukes. They might not have even noticed the transporter beam last time. I'm pretty sure they'd actually have to be actively looking for it to detect it."

"Pretty sure?"

"Okay, I'm sure. Does that make you feel better?"

"No."

"Well it's all I've got. Anyways, I'm ready to go when everyone else is. Transport us to the armory near the dart bay."

"Will the schematics we have work on ten thousand year old ships?"

"Yes. They were sleeping most of that time. Not like they were adjusting their design specs all that much."

"Got it. Are you two ready?"

"Yes." Sheppard and Teyla said in unison. The two disappeared in a flash of light and appeared inside the ship. The compartment they were in was full of wraith weapons.

"Make sure to grab enough stunners for the other us to help out." Rodney said.

"Can you be so sure they will help us?" Teyla wondered as she grabbed a stunner and slotted another into her belt.

"They're us. You shouldn't need to ask that question."

"The other me definitely won't pass up the opportunity to stop Todd." Sheppard commented. "But that doesn't matter right now. They'll be here any minute, and I want to be in position."

"I am prepared." Teyla said.

"Yep, me too." Rodney confirmed.

"Well, lead the way."

"On it."

They exited the armory through the door and into the hallway. Rodney navigated them through the ship towards the dart bay as quickly as possible. He stopped them once they were nearby.

"We're a little late but it's okay. They're bringing us right toward us." McKay said. "I can't tell whether Todd is there or not. All I know is I'm detecting four human life signs headed this way."

"Take cover behind the walls here. When they get close, you two can blindly fire into the hallway." Sheppard ordered.

"Where are you gonna go?"

"I'm going to go around and take them from behind. Just hold them here until then."

"Okay. Sounds good."

"Good luck John. Be careful." Teyla said.

"I always am…" He replied before starting into another hallway. He stopped. "Oh, and aim high. We don't want to give ourselves a double whammy when we should be waking up soon."

With that said, he took off.

"I will fire on your lead Rodney." Teyla said as she hid herself against the wall so that she could not be spotted from the hallway. McKay nodded as he did the same, not taking his eyes off of the lifesigns detector as he waited for the right time to attack. When he saw them approaching close enough, he raised his hand and silently counted down from five. When he hit zero, both of them pointing their stunners around the wall and opened fire. The initial storm of stun bolts caught several wraith off guard as the others returned fire while retreating.

Only they backed up right into Sheppard who swung from around the wall and took them from behind. He managed to take out three before they turned around to attack him.

"Push them now!" John called out to his allies as he returned fire from around his wall. Teyla moved up from her position and into the hallway, cleaning up the last of the active wraith warrior drones. "Nice."

Rodney joined them as they dug through the ocean of unconscious wraith to find themselves. It didn't take them long, all lying face up and unconscious.

"Let's find those ZPMs and get a beacon on them." Sheppard ordered. "Then we can hide them in an empty room and the Daedalus can beam them at the same time as us."

"They should still be in my bag… and here it is." Rodney said as he pulled it from the hands of an unconscious wraith. He dug through it and managed to find the ZPMs. With that, he dropped a tracking beacon (configured with a signal only the future Daedalus could detect). "I'll just leave the whole bag so the other me doesn't get suspicious when we tell him it's somewhere else."

"Teyla why don't you take the bag and go put it somewhere while we work on waking these guys up?" John asked. "Anywhere out of sight is fine, we won't be here long. And don't go far. They'll get suspicious when these guys show up and I don't want you caught by yourself."

"Very well." She said with a nod, taking the bag from Rodney and heading out of the hallway.

"We didn't wake up until at least twenty minutes after this. What's the plan?" Rodney asked.

"It's a simple but effective one." John said kneeling down beside the past Rodney. He wound up, and slapped him across the face. Hard.

"Ow." Both Rodney's said simultaneously, rubbing their cheek. Though at widely different volumes as the past McKay sat up in a flash.

"What the hell was that for!?" The past Rodney asked looking at Sheppard.

"Time to wake up sleepyhead."

"You could've tried shaking me!"

"It was too good an opportunity to pass up."

"What's going on? How did you-?"

The past Rodney trailed off as he noticed the presence of not only the future Rodney, but the past Sheppard.

"Hi." John said with a little wave. "We're from the future."

"Oh, nonononono. That must mean something went very wrong."

"You could say that. But, uh, we don't have much time to talk. We need to wake the others up and get moving."

"Why?"

"We need to stop Todd from killing his past self and taking over the galaxy." The future Rodney answered. "Or at least, that's what the future looked like when we went there."

"Wouldn't he…?" The past Rodney started to ask.

"Disappear? Yea, that's what we thought, but being in the past…"

"Stops the alternative reality effect? What if…?"

"Yea I thought we might also be shielded from…"

"Paradox."

"Exactly."

"Ugh… I'm just going to wake the other me up." Sheppard said moving to the past Sheppard. He shook the man's shoulders a bit. "Wake up sunshine. It's time to get up."

The past Sheppard's eyes slowly opened. Upon waking up and seeing himself waving at him, he jumped back with a start.

"Not again…" The past John said. "So, what is it this time?"

"We're from the future." The future John answered.

"Where is the other me, then…?" The past Teyla wondered as she woke up. "Or the other Ronon, for that matter…"

"He's in our Daedalus' infirmary." The future Teyla answered as she reappeared. "Speaking of, you might want to call your Daedalus and send him back. He is not well."

The past Teyla went over to the past Ronon to confirm this, and nodded. The past Sheppard went and dug his radio out from the Wraith.

"Daedalus, this is Sheppard." John said.

"It's good to hear from you. We were starting to fear the worst." Caldwell responded. "We're here to render any assistance you need. Maybe I can offer a distraction so you can escape? You know, since we can't beam you…"

"That was a lie Todd forced Ronon to tell you." The future Rodney said.

"Todd made Ronon say that. It's safe to beam us, but we can't go just yet… we've gotta get Todd back. You should at least beam Ronon. He needs medical attention."

"But what about the beaming limit imposed by Doctor McKay? If I beam Ronon now, I won't be able to beam you later."

"We're going to have to go over it." The future Rodney said.

"Couldn't we escape in a dart?" The past Rodney asked.

"That was what I was thinking, but there's no guarantee we'll be able to get there after we stop Todd."

"Yes, I see your point… besides, they might not have even detected the beam. It's not like they're actively looking for it right now."

"Exactly."

"He says it's fine now." The past Sheppard replied.

"I'm guessing it's more complicated than that." Caldwell said.

"Yea… Sheppard out." The past Sheppard said as he stood up. "So… what's the plan?"

The future versions of the team handed the past versions their extra stunners.

"We have to storm the throne chamber and capture Todd before he kills his past self." Rodney said.

"Of course, killing him would also be just fine in my book." Sheppard replied.

"That's a thought." The past Sheppard said.

"What about the-?" Past Rodney started to ask.

"Not now Rodney. I'm assuming you're mine."

"Yea."

"Anyways, your plan sounds good… uh… John."

"I thought you'd like it… John." The future Sheppard replied.

"This kind of stuff never stops being weird."

"Just another day at the office."

"Ha, you've got a point."

The two Teyla's seemed satisfied to give a stoic nod to each other.

"What about the ZPMs?" Past Rodney asked.

"They weren't with you. They must be keeping them somewhere else." Future Sheppard said. "I bet you the guards that took Todd have it."

"Wow. I can't believe they actually searched for them."

"There's always a first. But, we don't have time."

"Well, at least we know we're successful." The past Rodney said.

"What do you mean?" Past Sheppard asked.

"If we failed then wouldn't another us show up right about now?" Future Rodney answered.

"That's only if we aren't dead." Future Sheppard responded.

"Oh… yea…"

"We must not assume our success." Future Teyla said.

"Agreed, it would only serve to have us make rash decisions." Past Teyla said with a nod.

"Either way, we need to stay quiet and get moving." Past Sheppard interjected. "McKay and McKay, get a move on."

"On it." Both McKay's said.

"So, you think we should…?" The past McKay asked pointing at the screen to decide a route.

"Yea that should work." The future McKay confirmed.

"This way folks." They both said in unison. "Ah, a man after- this is weird."

"Just go." Both Sheppard's said in unison, causing them to look at each other.

"Yep, totally weird…" Past Sheppard said as he followed the McKays.

Once everyone had fallen silent, progress was quickly made as they cut across the ship. Once they were approaching the throne chamber and found a fork in the road, both Sheppard's spoke up at exactly the same time.

"We'll split up here." They both said. They looked at each other, and both continued speaking dubiously. "We'll meet back up inside…"

"We understand the plan." Both Teyla's said in unison.

"I must say, I understand their feelings. This is very strange." Past Teyla said.

"I feel the same." Future Teyla said.

"Anyways, we have a plan, so let's do it." Future Sheppard said.

"I was just about to say that…" Past Sheppard started.

"…but you thought better of it."

"Yep… See you on the other side."

"Hopefully this doesn't take long. This is creeping me out a little too much."

"Something else we agree on. Okay, so my team, let's go." Past Sheppard said.

"Which Sheppard are you?" Past McKay wondered.

"Uh… the… one that didn't go into the future." He answered.

"Oh, good, you're mine."

"Did you really have to phrase it like that?"

"What?"

"Never mind. Coming Teyla?"

"Yes." Past Teyla responded joining them. They started down the hallway.

"We'll be on Channel 3." Future Sheppard said fiddling with his radio. "Tell me when you're in position with three clicks."

"Will do." Past Sheppard replied. Future Sheppard signaled his own team with his hand, having them follow up the corridor until they were near the throne room. They encountered several warrior drones on the way and managed to clear them without issue. Past Sheppard's team were in position first as they gave the three click signal. Once future Sheppard's team was also in position around the door.

"Go!" Future Sheppard gave the order as they went in.

"So young, and so foolish." They heard Todd say as they entered and opened fire with stunners. It took both teams mere seconds to clear the room. The explosion didn't rock the planet below and shake the ship until they were already finished.

"Huh, that was easier than I thought it would be." Past Sheppard said as he lowered his weapon.

"Rodney, get a beacon on our Todd."

"Which one is that?" Future Rodney asked.

"The one who just talked. So, it would be the one on bottom…"

Both Todd's were lying on top of each other. Rodney extricated the one on bottom and placed a beacon on him.

"Too bad we couldn't kill him." Past Sheppard said. "But I guess that wouldn't be very gracious of us. So we'll let you guys have him. Now, we just have to find the ZPMs… Where do you think they put them McKay?"

"Probably the armory." Past McKay answered. "But I can't know that. They could've put my bag anywhere if they knew what those things were. Were the ships you encountered in the future…?"

"ZPM powered?" Future Rodney asked. "Yes."

Future Sheppard gave him a little glare.

"But… uh… it wasn't from us." Future McKay continued. "They must've gotten some other ZPMs because we have ours. Todd gave them to us when he let us go."

"Long story short, we've got what we need." Future Sheppard said.

"Anyways, uh… me. Set your Time Travel Drive to exactly one second after we left." Future Rodney said.

"Oh, so we get distinct timelines. It would be pretty awkward with two of us all around."

"Yep."

"Will do."

"First we've gotta get those ZPMs." Past Sheppard said. "We can't just let the Wraith keep them or that future you saw before might happen anyways."

"Uh, we were hoping to leave now…" Future Sheppard said. "But… I guess you've got a point."

"There's something they are not telling us." Past Teyla said. "First it was their Rodney, now it is him…"

"Yea I picked up on that." Past Sheppard said.

"It is true that we are not telling you the full story." Future Teyla said, attempting to defuse the situation before it became volatile.

"Todd didn't really give you guys the ZPMs, did he?" Past McKay asked. "He stole them from our bag."

"Yes… and you know why we can't give them back to you." Future Sheppard said. "I'm sorry but if you want ZPMs you'll have to get your own."

Just as the past version of Sheppard was about to continue the argument, a wraith stun blast suddenly came from the door. He barely managed to duck in time as a storm of Wraith warrior drones entered. Both teams drew out their P90s and opened fire. There were too many for them to take on. Especially as the explosion rocked the planet below and unsteadied their aim.

"Guess they were getting reinforcements together…!" Future Sheppard yelled over the gunfire. "I'm sorry about the ZPM's, but we've both gotta get out of here!"

"Fine!" Past Sheppard replied. He opened a channel to his Daedalus. "Daedalus! Beam us out now! We're going to get overwhelmed!"

Future Sheppard did the same, and said the same thing except for adding that they should beam the ZPMs. It was only seconds before both teams disappeared in flashes of light. But something went wrong during the transference. The original Sheppard's team, along with the bag that had the ZPMs, flew out of the beam onto the bridge of the Daedalus, rather than appearing normally. They were thrown into the bridge consoles.

"What the hell?" Sheppard wondered. The ship suddenly shook and the bridge sparked as the Wraith Hive Ships opened fire.

"Switch to shields now!" Caldwell called. "We're still close to that moon, hide us behind it!"

"Setting course now!" Bishop assured him.

"What happened!?" McKay asked as he stood up.

"When we beamed you the system overloaded." Marks answered. "Colonel, our shields still haven't recovered! They're already down to ten percent!"

"Then don't waste time returning fire! Just get every ounce of power to the shield!" Caldwell ordered.

"It overloaded?" Rodney wondered out loud. "Oh, no… I should've thought of that!"

"What is it Rodney?" Teyla asked.

"When we beamed at the same time as the other us… our beaming technology is the exact same. It operates on the same wavelength. There must've been a conflict. The system had to overcompensate to resolve the issue and make sure we all arrived at our destination. That power spike gave away our position."

"I guess time confuses the best of us." Sheppard said.

"Can't argue with you there."

"You can talk later." Caldwell interrupted. "I need you to get to the Time Travel Drive and configure the destination Doctor McKay."

"I'm on it. Teyla, grab those ZPMs and bring them down to engineering, could you?" He said running off. "I've got to get down there fast."

"Very well! I'll be right behind you!" Teyla called after him as she grabbed the bag.

"Meanwhile, I'm going to take Todd back down to the brig." Sheppard said grabbing the unconscious Todd on the floor and starting to drag him.

"We've successfully escaped behind the moon." Marks said as Sheppard exited the bridge. "The enemy no longer has a targeting solution."

"How long until they catch up?" Caldwell asked.

"Ten minutes at most."

"Not much time…"

"Colonel Caldwell, do we have the hyperdrive?" Rodney asked over the radio.

"Why do we need that?" Caldwell inquired. "Just activate the Time Travel Drive and let's get out of here."

"We can't do that!"

"Why not?"

"Because, we can't use the Time Travel Drive in the proximity of this moon. I started a scan on its composition when we got here. There's a high likelihood it could interrupt us because of its unique magnetic field. The way it interacts with the drive's internal components could cause problems. So it would be best if we jumped forward from somewhere else."

"Marks, what's the status of the hyperdrive?" Caldwell asked.

"It's still offline. We've been working on fixing it since we were attacked in the future, but it doesn't look like it's going well. It'll be hours."

"Can we put some distance between us and the Hive Ships?"

"We'll still be in weapons range if we leave the radius of the moon."

"Damn it. Doctor McKay, we can't survive another engagement with those Hive Ships. What happens if the moon interrupts the function of the drive? Do we just not jump?"

"I honestly have no idea. We've never tested the drive in this environment."

"We're going to have to risk it. If those Hive Ships catch up, we're dead anyways."

"Alright… I'm setting our destination right now. Activate the drive on my mark."

"I'm ready when you are Doctor McKay." Marks assured him. "You might want to hurry. The Hive Ships will round the moon and be able to open fire on us within the next three minutes."

"I'm going as fast as I can… and… there! Go ahead! Activate the drive!"

"Engaging now."

The Daedalus disappeared from the past and reappeared in the future.

"Drive activation successful. The enemy Hives have disappeared from sensors." Marks said.

"Good job Doctor McKay." Colonel Caldwell said over the radio.

"Don't congratulate me. We've got a problem." Rodney said over the radio.

"What is it?"

"The drive burned out from being forced to make the jump in those conditions."

"We have what we needed. I don't see how that's a problem."

"Do you remember how we showed up in the past about ten minutes later than we wanted?" McKay asked.

"Yes. What about it?"

"I've configured the drive to give me more feedback and it looks like the targeting program Zalenka and I made for the device had a fatal flaw. Something we didn't know when we made the bigger version for the Daedalus." McKay began to explain.

"You see, while we expanded the field to encompass the Daedalus, we didn't reconfigure the field to act properly on a larger object." Zalenka said.

"So? What? Were we ten minutes off?" Caldwell wondered. "That's not really a problem Doctor McKay."

"We only would've been if it weren't for an aggravating problem." McKay continued. "The magnetic field of the moon we were orbiting disrupted the drive, and it aggravated the variance of the Time Travel Drive when we jumped."

"What are you saying?" Caldwell asked.

"We overshot our destination by two years. We left in the year 2010, but we've arrived in the year 2012. And with the Time Travel Drive burnt out, we have no way home."

* * *

 _ **STARGATE ATLANTIS: JOURNEYS FOR PEGASUS**_

 _ **A Fan-Written Conclusion to Stargate: Atlantis**_

 _ **Stargate initially conceived by…**_

 _ **Roland Emmerich**_

 _ **Dean Devlin**_

 _ **Television Show originally created by…**_

 _ **Brad Wright**_

 _ **Robert C. Cooper**_

 _ **Writing ideas gleaned from…**_

 _ **Johnathan Mallozzi**_

 _ **Written by…**_

 _ **Niko DelValle**_

* * *

 _ **All copyrights belong to their respective owners.**_

* * *

 _ **NEXT TIME ON STARGATE ATLANTIS**_

AR-1 has become stuck in the future. With no other options, they decide to return to Earth with the ZPMs retrieved from the past, albeit two years later than they imagined. They find the conditions on their home planet far more problematic than when they left, and they find that the Atlantis expedition has gone on without them in a way they never could've imagined.


End file.
